TB-Profiler result

Run: SRR11823427
Summary

Run ID: SRR11823427

Sample name:

Date: 03-04-2023 04:57:54

Number of reads: 1361902

Percentage reads mapped: 99.76

Strain: lineage4.9

Drug-resistance: Sensitive

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.9 Euro-American (H37Rv-like) T1 None 1.0
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrA 6922 c.-380G>T upstream_gene_variant 0.14
fgd1 490937 p.Pro52Arg missense_variant 0.12
mshA 576750 p.Lys468Thr missense_variant 0.25
rpoB 759620 c.-187A>C upstream_gene_variant 0.38
rpoB 760116 p.Pro104Thr missense_variant 0.13
rpoB 760958 c.1152G>C synonymous_variant 0.25
rpoB 761152 p.Leu449Gln missense_variant 0.12
rpoB 763203 p.Ser1133Ala missense_variant 0.13
rpoC 763652 p.Ile95Leu missense_variant 0.19
rpoC 766856 p.Arg1163Cys missense_variant 0.13
mmpL5 777036 p.Gln482Met missense_variant 0.17
mmpR5 779317 p.Ala110Thr missense_variant 0.12
fbiC 1302817 c.-114C>T upstream_gene_variant 0.11
fbiC 1305126 c.2196T>C synonymous_variant 0.1
embR 1416430 c.918G>C synonymous_variant 0.13
embR 1417261 c.87A>G synonymous_variant 0.17
embR 1417268 p.Pro27Gly missense_variant 0.17
embR 1417276 c.72C>T synonymous_variant 0.27
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474425 n.768A>G non_coding_transcript_exon_variant 0.33
rrl 1474428 n.771C>T non_coding_transcript_exon_variant 0.35
rrl 1476683 n.3026T>C non_coding_transcript_exon_variant 0.13
inhA 1674963 c.762G>T synonymous_variant 0.12
rpsA 1833636 p.Tyr32Ser missense_variant 0.16
rpsA 1833641 p.Asn34Asp missense_variant 0.2
rpsA 1833648 p.Gly36Val missense_variant 0.25
rpsA 1833651 p.Asp37Ala missense_variant 0.25
rpsA 1833658 c.117C>T synonymous_variant 0.26
rpsA 1834166 p.Gly209Ser missense_variant 0.13
katG 2156447 c.-336C>T upstream_gene_variant 0.12
PPE35 2170035 p.Val193Ala missense_variant 0.19
pncA 2289379 c.-138T>G upstream_gene_variant 0.17
kasA 2518338 p.Leu75His missense_variant 0.13
kasA 2518348 c.234A>T synonymous_variant 0.33
kasA 2518368 p.Arg85Gln missense_variant 0.14
kasA 2518606 c.492G>C synonymous_variant 0.16
kasA 2518609 p.Met165Ile missense_variant 0.17
folC 2747399 p.Ile67Thr missense_variant 0.17
folC 2747526 p.Ala25Ser missense_variant 0.25
folC 2747531 p.Glu23Ala missense_variant 0.25
pepQ 2859701 p.Gly240Arg missense_variant 0.11
thyA 3074419 p.Lys18Arg missense_variant 0.11
thyA 3074648 c.-177T>G upstream_gene_variant 0.29
thyA 3074654 c.-183T>C upstream_gene_variant 0.21
fbiD 3339744 c.627A>C synonymous_variant 0.12
Rv3083 3449712 c.1209C>T synonymous_variant 0.13
Rv3083 3449747 p.Asp415Gly missense_variant 0.11
fbiB 3642167 c.633G>C synonymous_variant 0.12
fbiB 3642751 p.Asp406Ala missense_variant 0.21
rpoA 3878520 c.-13A>G upstream_gene_variant 0.1
rpoA 3878567 c.-60C>G upstream_gene_variant 0.32
rpoA 3878599 c.-92C>G upstream_gene_variant 0.27
clpC1 4040165 c.540G>T synonymous_variant 0.19
embC 4242378 c.2516_2517insC frameshift_variant 0.12
embB 4245695 c.-819C>A upstream_gene_variant 0.12
embB 4246544 p.Thr11Pro missense_variant 0.19
embB 4246548 p.Pro12Gln missense_variant 0.32
embB 4246555 c.42G>C synonymous_variant 0.27
embB 4246556 p.Ala15Pro missense_variant 0.27
embB 4246563 p.Leu17Trp missense_variant 0.23
embB 4246567 c.54G>T synonymous_variant 0.15
embB 4249744 c.3231G>A synonymous_variant 0.18
embB 4249751 c.3238T>C synonymous_variant 0.18